Prime Minister Naftali Bennett accused Tehran of "trying to shirk responsibility" for Thursday's incident, and called its denial "cowardly".
Speaking during a weekly meeting of his cabinet on Sunday, Bennett said: "I declare unequivocally: Iran is the one that carried out the attack on the ship," adding that intelligence supports his claim.
"We, in any case, have our own way to relay the message to Iran," Bennett said. Israel's foreign minister said earlier the incident deserved a harsh response.